chr16-87604287-CCTGCTGCTGCTGCTGCTGCTG-C

Variant names:

• chr16-87604287-CCTGCTGCTGCTGCTGCTGCTG-C
• rs71156237
• NM_020655.4:c.382+781_382+801delCTGCTGCTGCTGCTGCTGCTG

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP3 BS2

The NM_001271604.4(JPH3):​c.452_472delCTGCTGCTGCTGCTGCTGCTG​(p.Ala151_Ala157del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000403 in 1,432,822 control chromosomes in the GnomAD database, including 5 homozygotes. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00067 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00037 (5 hom.)
• Consequence: JPH3 NM_001271604.4 disruptive_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.966
• Publications: 1 publications found

Genes affected

JPH3 (HGNC:14203): (junctophilin 3) Junctional complexes between the plasma membrane and endoplasmic/sarcoplasmic reticulum are a common feature of all excitable cell types and mediate cross talk between cell surface and intracellular ion channels. The protein encoded by this gene is a component of junctional complexes and is composed of a C-terminal hydrophobic segment spanning the endoplasmic/sarcoplasmic reticulum membrane and a remaining cytoplasmic domain that shows specific affinity for the plasma membrane. CAG/CTG repeat expansion from normally 6-28 repeats to 40-59 repeats in the 3' UTR of this gene have been associated with Huntington disease-like 2 (HDL2). This gene is a member of the junctophilin gene family. Alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Jul 2016]

JPH3 Gene-Disease associations (from GenCC):

• Huntington disease-like 2

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, Ambry Genetics

ACMG classification

Our verdict: Likely_benign. The variant received -5 ACMG points.

• BP3: Nonframeshift variant in repetitive region in NM_001271604.4
• BS2: High AC in GnomAd4 at 101 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001271604.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JPH3	NM_020655.4	MANE Select	c.382+781_382+801delCTGCTGCTGCTGCTGCTGCTG		intron	N/A	NP_065706.2
	JPH3	NM_001271604.4		c.452_472delCTGCTGCTGCTGCTGCTGCTG	p.Ala151_Ala157del	disruptive_inframe_deletion	Exon 2 of 2	NP_001258533.1	F8W9A3
	JPH3	NM_001271605.3		c.*150_*170delCTGCTGCTGCTGCTGCTGCTG		3_prime_UTR	Exon 2 of 2	NP_001258534.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JPH3	ENST00000284262.3	TSL:1 MANE Select	c.382+781_382+801delCTGCTGCTGCTGCTGCTGCTG		intron	N/A	ENSP00000284262.2	Q8WXH2-1
	JPH3	ENST00000301008.5	TSL:1	n.712_732delCTGCTGCTGCTGCTGCTGCTG		non_coding_transcript_exon	Exon 2 of 2
	JPH3	ENST00000537256.5	TSL:2	n.96+2379_96+2399delCTGCTGCTGCTGCTGCTGCTG		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.000674 AC: 101 AN: 149958 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000173

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000132

Gnomad ASJ AF: 0.0145

Gnomad EAS AF: 0.000197

Gnomad SAS AF: 0.00106

Gnomad FIN AF: 0.000388

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000445

Gnomad OTH AF: 0.000974

GnomAD4 exome AF: 0.000372 AC: 477 AN: 1282756 Hom.: 5 AF XY: 0.000355 AC XY: 225 AN XY: 632940

African (AFR) AF: 0.000106 AC: 3 AN: 28322

American (AMR) AF: 0.0000926 AC: 3 AN: 32392

Ashkenazi Jewish (ASJ) AF: 0.00846 AC: 183 AN: 21628

East Asian (EAS) AF: 0.00 AC: 0 AN: 24078

South Asian (SAS) AF: 0.000180 AC: 14 AN: 77812

European-Finnish (FIN) AF: 0.000272 AC: 8 AN: 29386

Middle Eastern (MID) AF: 0.000395 AC: 2 AN: 5062

European-Non Finnish (NFE) AF: 0.000227 AC: 230 AN: 1013012

Other (OTH) AF: 0.000666 AC: 34 AN: 51064

GnomAD4 genome AF: 0.000673 AC: 101 AN: 150066 Hom.: 0 Cov.: 0 AF XY: 0.000656 AC XY: 48 AN XY: 73222

African (AFR) AF: 0.000172 AC: 7 AN: 40668

American (AMR) AF: 0.000132 AC: 2 AN: 15150

Ashkenazi Jewish (ASJ) AF: 0.0145 AC: 50 AN: 3448

East Asian (EAS) AF: 0.000198 AC: 1 AN: 5062

South Asian (SAS) AF: 0.00106 AC: 5 AN: 4710

European-Finnish (FIN) AF: 0.000388 AC: 4 AN: 10302

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.000445 AC: 30 AN: 67458

Other (OTH) AF: 0.000963 AC: 2 AN: 2076

Alfa AF: 0.00 Hom.: 316

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.97
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs71156237; hg19: chr16-87637893;